Table 7 Clustering analysis of RNA aptamers against CD2 to identify related sequence and structure groups.

From: High throughput sequencing analysis of RNA libraries reveals the influences of initial library and PCR methods on SELEX efficiency

Group

CD2 aptamer

30-nt random sequence

Reads of each group (in top 50 unique sequences)

Frequencies of each group (in top 1000 unique sequences)

 

Initial library

Round 3

Round 5

Round 6

Round 7

Initial library

Round 3

Round 5

Round 6

Round 7

1

H-1

TTTCCCAACGCACTTCCTCGAGTTGTTGGC

0

16,311

1,326,301

2,947,944

6,655,972

0.00%

5.00%

19.60%

31.91%

41.13%

↑

2

H-2

TCCCAACATCGTTTTAATTGTCGTAGTGTG

0

32,869

1,518,857

2,737,139

5,798,090

0.00%

10.08%

22.45%

29.63%

35.83%

↑

3

H-3

TCCATCGTCTCTTATCGTCTCTTGTCGCGC

0

77,956

1,202,986

1,384,237

722,365

0.00%

23.90%

17.78%

14.98%

4.46%

↓

4

H-4

AATTTCCTCAACCGCGTCCATTGTCGTGTG

0

15,669

763,432

148,000

770,723

0.00%

4.80%

11.28%

1.60%

4.76%

↗↘

H-10

AATTCGTCAAAGTCGTTTATTTCGTCTGTG

0

1,118

14,494

14,547

0

0.00%

0.34%

0.21%

0.16%

0.00%

↓

5

H-5

AAATGTTTTTCGATCCTTTTAGTCGCTGCA

0

30,611

451,752

285,503

380,099

0.00%

9.38%

6.68%

3.09%

2.35%

↓

6

H-6

CACGCACGATGGATTGTTGTCTGGCCACCA

0

103,828

517,706

716,614

338,580

0.00%

31.83%

7.65%

7.76%

2.09%

↓

H-12

TCCGCGAGTTCATTGAGTTGTTGCGCCCCA

0

1,364

0

11,418

0

0.00%

0.42%

0.00%

0.12%

0.00%

↓

7

H-7

ATTCCTCAAATTCATCGATCTCGTCTGGTG

0

2,580

76,991

87,753

184,665

0.00%

0.79%

1.14%

0.95%

1.14%

↓

8

H-8

TTTCGTCCTGAGTTCGTGTCCTCGTCTGTG

100

6,839

151,921

92,818

102,527

3.16%

2.10%

2.25%

1.00%

0.63%

↓

9

H-9

TCCTGGTGTTGTTGGTTGTCTGCGCTGCCC

0

5,000

25,636

38,412

38,318

0.00%

1.53%

0.38%

0.42%

0.24%

↓

10

H-11

TTTCGTCTTTTTATCGTTCCTATGTCGCTG

0

488

10,372

8,303

0

0.00%

0.15%

0.15%

0.09%

0.00%

↓

11

H-13

CACCTACACCCCGCTATTGGTCGTTGTGCA

0

317

0

0

0

0.00%

0.10%

0.00%

0.00%

0.00%

↓

Others

 

Orphan sequences

189

0

0

0

0

5.96%

0.00%

0.00%

0.00%

0.00%

↓

  

Total reads of all the groups

289

294,950

6,060,448

8,472,688

14,991,339

      
  1. After alignment of the top 50 sequences, several groups of RNA aptamers were identified. The representative RNA aptamers, the reads of each group, and their frequencies in the top 1000 unique sequences were listed. Only the 30-nt random sequences of the aptamer core regions (5′-3′) are indicated.
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